The game starts showing a black screen, with an adult Clementine Everett narrating "Years ago, there was a Conflict named the War Against the Villain Armada. Nobody remembers how, or why... It started. But the Forces of two Factions, The Hero Coalition and The Villain Armada, were always there to balance their power within our Physical Plane, The Multiverse. In some Realities, it ended in our Victory, others in the Armada's... But what if there was one where neither side triumphed over the other?" as the game shows a Hologram of Earth, which reads 'Earth-CE120 - Outer Realities, Coalition-Armada Status: Engaged. Battle of San Francisco underway, all Ground, Air and Sea Forces ready to deploy conclusively.' as the Hologram labels an Coalition-Class Dreadnought Ship within the Low Earth Orbit above San Francisco, and then zooms in on the Coalition Ship and marks it as 'USS Retribution - Coalition Dreadnought, Registration #52775. Crew Onboard: 60,000. Fighter Jets and Carriers: 65,000. All Systems online, ready for Battle against Armada Destroyer 'Olympus Mons'.' and then the game switches to inside the USS Retribution, showing a 14-year-old Clementine sleeping in her Personal Crews Quarters as an Alarm blares across the Dreadnought Ship, and then the PA announces "Crew, we are ready to engage the Olympus Mons! All hands to Battle Stations!" as Clementine gets up and starts running towards the Command Bridge with several other Heroes such as Jackson Pearce, Kyle Reese, Tyler Green and Dashiell 'Dash' Parr. Clementine then says "The Battle of San Francisco's absolutely chaotic down there, guys! It's the most intense Battle of The War of The Multiverse!" and Jacks tells her "Guess we'd better just go with the flow, Clem. Don't worry, San Francisco will be liberated and The Villain Armada will fall today!" as they walk on to the Command Bridge, seeing the Coalition Spacefleet fighting against the Armada in an intense Space Battle, with Ships of all Classes on both sides firing Lasers and being absolutely destroyed by the Battle of Earth-CE120, and a Hologram shows the Battle of San Francisco on Earth: Ships falling from the Sky, Soldiers dying, Tanks and Aircraft exploding and already-destroyed Skyscrapers being absolutely ripped apart by the Final Battle between the United Dimensions Coalition and The Villain Covenant. Clementine then sees the Armada Destroyer 'Olympus Mons' on the Hologram and says "We've got a VillAr Destroyer operating in Low Orbit, it's tearing our Fleet apart. We need to coordinate a Takedown Op with our Jackal Fighters, infiltrate the Ship and destroy it! We succeed, and our Forces in San Francisco will get an even better chance!" as the Squad moves towards the Docking Bay in order to proceed with their part in the Battle of San Francisco.

A few minutes later, Clementine is seen loading up her Weapons such as her NV-4 Assault Rifle, EE-30 Plasma Rifle and Laser Railgun in her Personal Quarters, and then she hears a young baby crying and turns around to see Jacks cradling an infant boy, saying "Shh, it's alright, little guy... I'm here." as Clementine holsters all her Weapons and sits down next to Jacks, asking "How is he? He alright?" and Jacks looks at the infant, who is actually his son Jake Pearce and answers "Yeah, he's alright. Might be sad that his Dad is gonna go off to War, but... You know, that's how all kids are." and Clementine responds "How old are you, 14? No offense, but you're way too young to have a kid." and Jacks looks at her and says "It was a mistake, Clem... It was just so stupid, but Jake's the best thing that ever happened to me." as he looks at Jake and laughs, before saying "He's got black hair, like his Mom. I'm worried about what he's gonna be like once he hits past 10 years old. Y'know, like you and me were?" and Clementine laughs, before holding Jake in her arms. Jacks then tells her "Look, Clem: The United Nations Multiverse Forces and The Villain Armada will always hate each other, there will never he Peace... Two sides of the same coin, that's what me and Jake are: Nephylum, a Hybrid of Hero and Villain." and Clementine looks him in the eyes, asking "What is it you want, Jacks? Just say it so we can get this Battle over with." as Jacks holds her hand and says "I want you to take care of Jake. In case I... In case something happens-" and Clementine says "Don't talk like that, Jacks! This Battle will be intense, yes... There will be Soldiers dying all around us, explosions left and right, Ships falling from Orbit: But I promise, that I will always be at your side and protect you, so that you can raise your son in peace. You are not leaving this boy today, understand?" and Jacks tells her "Swear to me! Promise me, that you will look after him in case something happens to me!" as he starts visibly tearing up, then sadly tells her "Please, Clem... I need you to promise me." and Clementine puts Jake down in a Bed, then kisses Jacks on the lips and wraps her arms around his neck, and then pulling away after a few seconds saying "I promise you, Jacks..." as the screen cuts to black.

The game then switches to several minutes later as Simon 'Ghost' Riley is heard saying "They're launching Skelters!!" as the game shows Clementine and several others piloting DATO-11 Fighter Jets given to them by the Dimensional Associated Treaty Organization, firing at several Armada Fighters and bringing them down as Jacks says "Attack those Frigates, now!!" as the Flight Team fires Photon Torpedoes at 2 Armada Frigates, which explode on Impact alongside several Fighters as Clementine and several others destroy even more Armada Fighters and Ships, before several DRO-80 Space Bombers launch an Airstrike on the Olympus Mons and destroy most of its Laser Turrets. Ghost then says "Shields are down, move in on the Olympus!!" as everyone ejects from their DATO-11 Fighters and then see the massive Battle between Coalition-Armada Fleets as several Armada Troops approach, and the Villain Slayers start killing them in a massive firefight, and Clementine grapples to Ship Debris and guns down Armada Troops from the side, jumping down off the Debris and grappling an Armada Grunt in mid-air, pulling him in and ripping the Mask off his Pressurized External Suit and then causing him to die in Space. Clementine then grapples down to the Exterior of the Olympus Mons as she and Jacks gun down even more Armada Troops, seeing an Armada Dropship as Jacks tosses a Plasma Grenade which explodes and kills several Soldiers while also destroying the Dropship as Clementine jumps into the aid and Grapples to the Ship Hull, gunning down even more Troops in a surprise Attack as she shouts "Everyone, keep pushing them back!!" as Dash responds "Heading for the Command Bridge, set C4 Charges!" and Tyler answers "Roger, moving in!!" as he runs across Ship Debris and guns down 3 Armada Troops with his ECDO-20 Plasma SMG, then uses his Grapple Hook to grab another Soldier and activate his Plasma Grenade, kicking the Soldier away and causing an explosion which destroys the Command Bridge, causing Armada Forces to get sucked out and into the Space Vacuum. The Team then moves into the Command Bridge and Clementine says "Dash, get to that Console and restore Gravity!" as Dash activates the Gravitational Field on the Dreadnought Ship and restores normal Gravity, and then Jacks says "You guys get back to the Fighters, get back down to the Battle of San Francisco. I'll move through the Dreadnought, kill anyone else aboard and find Scarecrow: He's onboard this Ship, I can sense him..." and then Clementine holds his hand and eyes him, saying "You promised me that you'd still be alive... Don't break that promise." and Jacks responds "I'll do my best... Take care of Jake for me, Clem." and Clementine kisses him on the lips one last time, then stops and puts her face up against Jacks', saying "I'll look after your son, I swear to you. But you will come back, right?" and Jacks kisses her again, before answering with "I'll do my best, now go..! Win this War, for The Hero Coalition, for The Multiverse... For us." and then the two move their separate ways, with Clementine, Dash, Kyle and Tyler all moving towards the Docking Bay with Jacks moving towards the Command Room of the Dreadnought. Jacks then looks out at Low Earth Orbit and sees the Spacefleets of both The Hero Coalition and The Villain Armada ripping each other apart in the epic Final Battle, and an Armada Command Chatter is heard saying "This is VillAr Fleet Command: All SpaceFleet Units, retreat from Orbit and head into Hyperspace to access the Unknown Realities!!" as what is left of the damaged Armada Fleet in Low Earth Orbit zooms off into Space using Emergency Hyperspace, while the Fleet Remains in San Francisco are all destroyed by the Coalition Forces, and then Jacks hears a banging noise and gunshots on the Blast Door behind him, then looks at the Command Console which says 'Warning: Ship Scuttle enabled. Verify this Command to destroy Ship due to Emergency Protocol.' as Jacks looks at the Console and sees an MR6 Pistol in his hands, before sighing and tearing up as the screen cuts to black and the Prologue ends.

The game then switches to 11 years later in the year 2028, showing a 25-year-old Clementine lying in her Bed inside a Woodland Cabin, and the Mission Text shows 'Haddonfield Mountains, Illinois - September 21st, 2028' as Clementine mumbles in her sleep, saying "Jacks, no... No, Jacks, don't... Please..." and breathing heavily as she suddenly wakes up sweating and breathing quickly after having a Nightmare about the War Against the Villain Armada. However, Clementine then hears a knock on her Door and says "Hang on, I'm coming." as she opens the Door to see an 11-year-old Jake Pearce standing there, looking much like Jackson Pearce when he was Jake's age: Pale-ish white skin and icy blue eyes but with long black hair, and Clementine asks "Jake? What are you still doing up, it's past midnight. It's, like... 2 AM right now." and Jake looks up at her and says "I, um... Heard you mumbling in your sleep again, and I heard you say that name again... Jacks." and then Clementine looks at the young boy (who doesn't know his father's name) and she sits down on her Bed and says "Sorry I woke you, little guy. You alright?" and Jake sits down next to her, looking at her with his deep, icy blue eyes and through bangs of long black hair. Jake then leans his head on Clementine's shoulder and Clementine wraps her arm around her adopted son's back, saying "I know that it must be stressful for you to live with me while I'm like this. Waking up in the middle of the night, hearing my Nightmares about the War, all the destruction it caused... Me thinking about your Dad." as Jake looks up at her and says "Yeah, well... We're living in the middle of the Woods, inside a Log Cabin where theoretically nobody can find us. So it's not all that bad." as he clears his hair out of his eyes, saying "Clem, I need to ask... What happened to my Dad? And who the hell is 'Jacks'?" and Clementine sighs in response. Looking at her adopted son with hesitation, she brings him closer and tells him "For decades, the Hero Knights guarded The Multiverse against the Forces of The Villain Armada, and before that nobody knows what caused the Merging of Dimensions which founded The Hero Coalition." and then she looks at Jake and says "Jacks was your biological father, he and your Mom were 14 when you were conceived in 2017." and Jake looks in slight shock, asking "So, Jacks was my Dad? And he was 14 when I was born. Jesus, well... What about my Mom?" and Clementine (upon hearing mention of Jake's mother) stays silent, but then simply tells him "It was after the Battle of Chicago, where the Coalition Forces surrounded The Villain Armada and broke the Armada Line in America. There was this massive Celebration Party in the Main Base afterwards, everyone was there, including your parents..." as she laughs morbidly, then explains "Your Mom and Dad, they had a little too much to drink that night... 10 fucking pints of Whiskey. And then later, when everyone else was busy still celebrating the Armada Defeat, your parents went to their Personal Quarters and, uh... They were having sex after the Celebration Party, nobody saw them do it, but then 2 weeks later, guess what?" and Jake asks "What?" as Clementine tells him "2 weeks later, your Mom took a Pregnancy Test. It was positive, and the look on Jacks' face when he found out was fucking priceless when your Mom went to him and says 'Hey, Jacks. I gotta tell you something: I'm pregnant', then his eyes looked like they were gonna fall from
their fucking sockets." as Jake asks her "They had... Sex? That's disgusting." and Clementine laughs and playfully punches him on the shoulder, saying "Aw, come on... I mean, it's natural and you'll probably be doing it in a few years." as Jake shudders and then laughs in almost hysterical humor.

A few minutes later, Jake is seen sitting at a Table as he eats from a plate, and then looks at Clementine and asks "Clem, what is this? This tastes absolutely amazing." and then Clementine responds "Glad you like it, Jake. It's a dead Cayote I caught a couple days ago." and then Jake keeps eating the cooked Cayote Meat, then asks "You killed a Cayote? Aren't they, like... Real ferocious?" and Clementine nods in response, then says "Yeah, besides you know I hate Canines anyway. Had a bad encounter with a Dog when I was 11, it bit me on the arm." as she rolls up her sleeve and shows the boy an old and healed scar on her arm. Jake then looks in shock and asks "A Dog bit you? What did you do to piss it off, steal Food from it?" and then Clementine explains "Well, it stole some Food from me and I tried to get it back... Immediately regretted that decision." as she hears a knock at the Door, then says "Stay here, Jake. I thought nobody knew we were here!" as she puts her hand towards her Gun Holster and then walks forward towards the Door, then opens it and sees James Pearce (Jackson Pearce's twin brother and Jake's uncle) standing there, and then James stands out in the rain and says "Hey, Clementine. You alright?" and then Clementine holsters her Glock 17 Pistol and then asks "James?! What the hell are you doing here, the United Dimensions Coalition and The Villain Armada will find us if you come here!" and then James tells her "Hey, relax. I've gone outta the Base, the UDC and IDF are too busy kicking each other's asses on the Front Line to follow me. Besides, even if they tried to go near you and Jake... I would kill them all." as Clementine pulls him inside and closes the Door behind him. Clementine then puts James against a wall and then says "How long's it been since we last saw each other?" and then James responds "About 8 months, and every day I thought about you... Your beautiful face, amazing body and those piercing yellow eyes that resemble mine." as Clementine wraps her arms around James' waist and then kisses him on the lips, holding the kiss for several seconds. As the two Hero Knights press their bodies against each other, James puts his arms around Clementine's lower back then moves his hands up towards Clementine's shoulders, but then the two separate as Jake enters the Room and asks "No way... Uncle James?!" and then he runs up to James and hugs him, and James embraces his nephew and lifts him up, saying "Hey there, little guy! Ah, I haven't seen you in almost a year!" as he looks at Jake then laughs, remarking "Wow, you've gotten so tall! Almost exactly like your Dad was..." as Clementine looks at Jake and says "Hey, go and finish your food. I'm gonna have a quick talk with your Uncle." as Jake walks back into the Kitchen, and then James looks at Clementine as the girl tells him "He takes after his Dad, y'know..." as she nuzzles his neck and kisses him, and then James laughs and says "Does he have anything similar to me?" as Clementine hugs him, putting her head on his chest and saying "He's got your attitude... And your persistence. He has an amazing kind of fire inside him!" and then James wraps his arm on Clementine's back and says "You and Jake are the two most important people in my life. I'm not gonna stop looking out for you..." and then Clementine laughs, before quickly saying "Hmm..." and then kissing James on the cheek just to whisper "Always looking out for us, huh?" as she kisses James on the lips and presses against him again, putting him up against a wall as Jake enters the Room and sees the two, clearing his throat before saying "Um... Guys? 11-year-old kid right here! Take it somewhere else..." as Clementine separates from James and looks at her adopted son before asking him "You finished eating, Jake?" and Jake nods in response, so Clementine tells him "Alright, well... You look real tired, so why don't you go upstairs and get some sleep?" as Jake says "Alright, but Hero Knights don't need sleep. I'll just leave you and Uncle James alone!" as he laughs and walks upstairs.

Clementine is then seen a couple hours later with James as she says "This matters, James. You being here... I just need to be sure that things are different from you. Y'know, that you won't be a Soldier anymore, you won't act like one around here... You'll just have to be a normal Civilian, and be a good Uncle to that boy." as she gives him a mug full of hot chocolate, then says "He's hit Jacks' age now. A lot like him, and that's what kinda worries me." as James drinks some of the hot chocolate and then says "You don't have to worry about him, Clem. Just take the reigns off of him, and let him express himself sometimes. If he wants to be like Jacks used to be... Then just let him." as he puts the mug down and says "Hot chocolate, huh? It's delicious, but I could do with something a little more... Stiff." as Clementine grabs a bottle of Whiskey and pours 2 glasses, before saying "Well, at least I know you're not a complete pussy when it comes to drinking." as the two drink from their glasses and then Clementine sits next to James after drinking a few more glasses. After a few seconds of looking into James' eyes lovingly, she kisses him on the lips as the two wrap their arms around each other and get closer, and then James asks "Do you think Jake's gotten to sleep..?" and Clementine answers "By now, he probably has. Think we should do the same?" as James laughs and then kisses her again. A couple minutes later, James and Clementine are seen in one of the Cabin Bedrooms, lying down in Bed and kissing as James wraps his arms around Clementine's lower back and puts his hands down the back of Clementine's jeans after unbuckling her belt and then Clementine takes her shirt off, before unbuckling James' belt on his pants as the two press their bodies against each other and start kissing intimately. James then takes Clementine's jeans off her and then moves his hands up to the strap of Clementine's bra, unbuttoning it as the two lie down in Bed and then start having sexual intercourse as the screen turns to black, but also showing the two during the intercourse several times such as Clementine kissing James on the lips and moving down to his neck, James sitting up and wrapping his arms around Clementine's naked body, holding her close and touching her bare breasts and after a couple more minutes, the two begin moaning in pleasure as they consummate their relationship.

The game then switches to the next morning as James wakes up in Bed as he sees Clementine sleeping next to him naked, with her arm spread across James' chest as James runs his hand up Clementine's bare back and starts running his hand through her long black hair (which has grown out since the events of the Walking Dead Crossover Series). Clementine then wakes up and exhaustedly says "Hey, babe." and then James responds "Hi, how'd you sleep?" and Clementine answers with "A lot better than I usually sleep, because you were here with me. Last night, though... Oh God, James, that was fucking amazing." as James laughs and then kisses her on the lips and moving down to her neck, while also moving his hands down from Clementine's shoulders and to her buttocks, before pulling away and saying "Clem, you might wanna get a Test done in a few days. Y'know, just in case this 'encounter' results in a little problem." as Clementine responds "James, it was just sex. Yes, a girl can get pregnant after one time... But not me." and James asks her "Remember what happened last time you had sex?" as he sits on the side of the Bed and starts putting his underwear back on. Clementine then puts the bed sheets around her still-naked body and wraps her arms around James, kissing his neck and saying "Don't bring that up, James... Please, Jake cannot find out who I really am. He's got too much of his father in him already, I do not want him picking up my personality traits. It could make him, well... Benevolent." as James looks her in the eyes and says "I'm sorry Clem, I just..." as Clementine gets up and starts putting her clothes back on, and James lies down in Bed as the former asks "So, why did you come back anyway? You're still a Soldier, and I let go of the New Multiverse a long time ago, I don't want any part in it." as she puts her bra and panties back on, saying "Jacks and I were the best Hero Knights in The Multiverse during the War Against the Villain Armada, but I left the New Multiverse behind after the Final Battle years ago... You remind me so much of Jacks, and I already lost one of my closest friends. I don't wanna lose you too, James." as she starts walking out of the Bedroom. However, James gets out of Bed and says "Alright, I'm gonna level with you: I left the New Multiverse because I wanted to go back to you and Jake... Because I wanted to live a peaceful life with you and I thought that maybe, since you've been raising Jake all on your own... Maybe we could have a child of our own?" as Clementine turns around and looks at him, and the Hero Knight says "Clem, you know that the Hero Knights are going extinct, and we're in desperate need of new ones in order to counter the IDF and their leader, Salen Kotch. And there's only 12 Hero Knights still capable of holding off the IDF Invasion of this Reality..." as Clementine looks at him in shock and with tears in her eyes, asking "So you had sex with me, hoping I would be impregnated with your child?! And then he or she, would become a part of the Multiversal Combat Recon Force?" and James responds "No, Clem, I would... We need more Hero Knights, Clementine. You above all should know that." and Clementine tells him "No, Pearce! The Villain Slayers crumbled after I left to raise Jake, and I will never rebuild the Team again. And even if we do have a child... That child will never be apart of any War, any Multiverse, none of it!!" as she walks towards him, tearing up and she says "I... I didn't mean that I don't want a kid with you. And I don't mean to hurt your feelings, I just... Never mind." as she starts walking away and then tells him "I'm going for a shower, I'll be down in a few minutes." as James responds "You mean 20 minutes. You always take long showers, Clem." as Clementine starts flirting with him, saying "Hey, you're welcome to join me in there if you want." as she giggles and then walks towards the Bathroom, and then James looks at several scars on Clementine's back and shoulders and remembers how she got them in the War Against the Villain Armada: A shrapnel explosion from a crashing VTOL during the Battle of Metroville (WOH: Legends), several Knife cuts from Armada Assassins during the Raid on Armada Central and being shot multiple times throughout the War with Bullets of varying Calibre.